Galaxy |

ARTIC guppyplex (version 1.7.3+galaxy0)

Structure of your input data:

Sequencing dataset(s) - one per sample:

Maximum read length:

Remove reads greater than this number of base pairs

Minimum read length:

Remove reads less than this number of base pairs

Minimum read quality:

Remove reads with average quality lower than this number. Set to 0 to skip the quality check.

The ARTIC guppyplex tool filters reads by length and (optionally) quality. This filter is typically used as a pre-processing step in the processing of amplicon sequencing Nanopore reads, where a size-based filter can be used to remove possibly-chimeric reads.

The default paramters of the tool (minimum length of 400 and maximum of 700) are based on the ARTIC amplicon scheme. If used with a different amplicon scheme they should be adjusted to use the minimum length of an amplicon as the minimum length and the maximum length of an amplicon plus 200 as the maximum length.

The tool can also be used simultaneously to gather partial fastq datasets into single datasets per sample.